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GMX-RMS(1)			     GROMACS			      GMX-RMS(1)

NAME
     gmx-rms - Calculate RMSDs with a reference structure and RMSD matrices

SYNOPSIS
	gmx rms [-s [<.tpr/.gro/...>]] [-f [<.xtc/.trr/...>]]
		[-f2 [<.xtc/.trr/...>]] [-n [<.ndx>]] [-o [<.xvg>]]
		[-mir [<.xvg>]] [-a [<.xvg>]] [-dist [<.xvg>]] [-m [<.xpm>]]
		[-bin [<.dat>]] [-bm [<.xpm>]] [-b <time>] [-e <time>]
		[-dt <time>] [-tu <enum>] [-[no]w] [-xvg <enum>]
		[-what <enum>] [-[no]pbc] [-fit <enum>] [-prev <int>]
		[-[no]split] [-skip <int>] [-skip2 <int>] [-max <real>]
		[-min <real>] [-bmax <real>] [-bmin <real>] [-[no]mw]
		[-nlevels <int>] [-ng <int>]

DESCRIPTION
     gmx rms compares two structures by computing the root mean square deviation
     (RMSD),  the  size-independent rho similarity parameter (rho) or the scaled
     rho (rhosc), see Maiorov & Crippen, Proteins 22, 273 (1995).  This  is  se-
     lected by -what.

     Each structure from a trajectory (-f) is compared to a reference structure.
     The reference structure is taken from the structure file (-s).

     With  option  -mir also a comparison with the mirror image of the reference
     structure is calculated.  This is useful as a reference  for  'significant'
     values, see Maiorov & Crippen, Proteins 22, 273 (1995).

     Option  -prev  produces  the comparison with a previous frame the specified
     number of frames ago.

     Option -m produces a matrix in .xpm format of  comparison	values	of  each
     structure in the trajectory with respect to each other structure. This file
     can  be  visualized with for instance xv and can be converted to postscript
     with gmx xpm2ps.

     Option -fit controls the least-squares fitting of the structures on top  of
     each  other:  complete fit (rotation and translation), translation only, or
     no fitting at all.

     Option -mw controls whether mass weighting is done or not.  If  you  select
     the option (default) and supply a valid .tpr file masses will be taken from
     there,  otherwise	the masses will be deduced from the atommass.dat file in
     GMXLIB (deprecated). This is fine for proteins,  but  not	necessarily  for
     other molecules. You can check whether this happened by turning on the -de-
     bug flag and inspecting the log file.

     With  -f2,  the 'other structures' are taken from a second trajectory, this
     generates a comparison matrix of one trajectory versus the other.

     Option -bin does a binary dump of the comparison matrix.

     Option -bm produces a matrix of average bond angle  deviations  analogously
     to the -m option. Only bonds between atoms in the comparison group are con-
     sidered.

OPTIONS
     Options to specify input files:

     -s [<.tpr/.gro/...>] (topol.tpr)
	    Structure+mass(db): tpr gro g96 pdb brk ent

     -f [<.xtc/.trr/...>] (traj.xtc)
	    Trajectory: xtc trr cpt gro g96 pdb tng h5md

     -f2 [<.xtc/.trr/...>] (traj.xtc) (Optional)
	    Trajectory: xtc trr cpt gro g96 pdb tng h5md

     -n [<.ndx>] (index.ndx) (Optional)
	    Index file

     Options to specify output files:

     -o [<.xvg>] (rmsd.xvg)
	    xvgr/xmgr file

     -mir [<.xvg>] (rmsdmir.xvg) (Optional)
	    xvgr/xmgr file

     -a [<.xvg>] (avgrp.xvg) (Optional)
	    xvgr/xmgr file

     -dist [<.xvg>] (rmsd-dist.xvg) (Optional)
	    xvgr/xmgr file

     -m [<.xpm>] (rmsd.xpm) (Optional)
	    X PixMap compatible matrix file

     -bin [<.dat>] (rmsd.dat) (Optional)
	    Generic data file

     -bm [<.xpm>] (bond.xpm) (Optional)
	    X PixMap compatible matrix file

     Other options:

     -b <time> (0)
	    Time of first frame to read from trajectory (default unit ps)

     -e <time> (0)
	    Time of last frame to read from trajectory (default unit ps)

     -dt <time> (0)
	    Only use frame when t MOD dt = first time (default unit ps)

     -tu <enum> (ps)
	    Unit for time values: fs, ps, ns, us, ms, s

     -[no]w (no)
	    View output .xvg, .xpm, .eps and .pdb files

     -xvg <enum> (xmgrace)
	    xvg plot formatting: xmgrace, xmgr, none

     -what <enum> (rmsd)
	    Structural difference measure: rmsd, rho, rhosc

     -[no]pbc (yes)
	    PBC check

     -fit <enum> (rot+trans)
	    Fit to reference structure: rot+trans, translation, none

     -prev <int> (0)
	    Compare with previous frame

     -[no]split (no)
	    Split graph where time is zero

     -skip <int> (1)
	    Only write every nr-th frame to matrix

     -skip2 <int> (1)
	    Only write every nr-th frame to matrix

     -max <real> (-1)
	    Maximum level in comparison matrix

     -min <real> (-1)
	    Minimum level in comparison matrix

     -bmax <real> (-1)
	    Maximum level in bond angle matrix

     -bmin <real> (-1)
	    Minimum level in bond angle matrix

     -[no]mw (yes)
	    Use mass weighting for superposition

     -nlevels <int> (80)
	    Number of levels in the matrices

     -ng <int> (1)
	    Number of groups to compute RMS between

SEE ALSO
     gmx(1)

     More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT
     2026, GROMACS development team

2026.3				  Jun 25, 2026			      GMX-RMS(1)
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